Inferring Cellular Networks Using Probabilistic Graphical Models

Science

Volumn 303, Issue 5659, 2004, Pages 799-805

  Friedman, Nir ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ASSAYS; DATA REDUCTION; GENES; MATHEMATICAL MODELS; PROBABILITY; SET THEORY;

COMPLEX CELLULAR NETWORKS; MOLECULAR ASSAYS;

MOLECULAR BIOLOGY;

MODELING;

BAYES THEOREM; GENE CONTROL; HUMAN; MATHEMATICAL MODEL; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; REVIEW; TRANSCRIPTION REGULATION;

BAYES THEOREM; CELL PHYSIOLOGY; COMPUTATIONAL BIOLOGY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MATHEMATICS; MODELS, BIOLOGICAL; MODELS, GENETIC; MODELS, STATISTICAL;

EID: 0842288337     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1094068     Document Type: Review

References (43)

1. E. Lander, Nature Genet. 21, 3 (1999).
2. S. Tavazoie, J. D. Hughes, M. J. Campbell, R. J. Cho, G. M. Church, Nature Genet. 22, 281 (1999).
3. Y. Pilpel, P. Sudarsanam, G. Church, Nature Genet. 29, 153 (2001).
4. R. Durbin, S. Eddy, A. Krogh, G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (Cambridge Univ. Press, Cambridge, 1998).
5. J. Pearl, Probabilistic Reasoning in Intelligent Systems (Morgan Kaufmann, San Francisco, 1988).
6. M. I. Jordan, Ed., Learning in Graphical Models (MIT Press, Cambridge, MA, 1998).
7. A glossary of this and other technical terms appears on Science Online.
8. W. Buntine, J. Artif. Intel. Res. 2, 159 (1994).
9. F. V. Jensen, An Introduction to Bayesian Networks (Univ. College London Press, London, 1996).
10. N. Friedman, L. Getoor, D. Koller, A. Pfeffer, Relational Data Mining, S. Dvzeroski, N. Lavrac, Eds. (Springer-Verlag, Berlin, 2001), pp. 307-337.
11. E. Segal, B. Taskar, A. Gasch, N. Friedman, D. Koller, Bioinformatics 17 (suppl. 1), S243 (2001).
12. Y. Barash, N. Friedman, J. Comp. Biol. 9, 169 (2002).
13. I. Holmes, W. Bruno, Proc. Int. Conf. Intell. Syst. Mol. Biol. 8, 202 (2000).
14. E. Segal, Y. Barash, I. Simon, N. Friedman, D. Koller, Proceedings of the 6th Annual International Conference on Computational Molecular Biology, G. Myers et al., Eds. (ACM Press, New York, 2002).
15. E. Segal, R. Yelensky, D. Koller, Bioinformatics 19 (suppl. 1), I273 (2003).
16. P. T. Spellman et al., Mol. Biol. Cell 9, 3273 (1998).
17. A. P. Gasch et al., Mol. Biol. Cell 11, 4241 (2000).
18. T. Lee et al., Science 298, 799 (2002).
19. E. Segal, H. Wang, D. Koller, Bioinformatics 19 (suppl. 1), I264 (2003).
20. M. Deng, T. Chen, F. Sun, Proceedings of the 7th Annual International Conference on Computational Molecular Biology, M. Vingron et al., Eds. (ACM Press, New York, 2003), pp. 95-103.
21. N. Friedman, M. Linial, I. Nachman, D. Pe'er, J. Comp. Biol. 7, 601 (2000).
22. D. Heckerman, D. Geiger, D. M. Chickering, Mach. Learn. 20, 197 (1995).
23. P. Spirtes, C. Glymour, R. Scheines, Causation, Prediction, and Search (Springer-Verlag, Berlin, 1993).
24. D. Pe'er, A. Regev, G. Elidan, N. Friedman, Bioinformatics 17 (suppl. 1), S21S (2001).
25. D. Pe'er, A. Regev, A. Tanay, Bioinformatics 18 (suppl. 1), S2S8 (2002).
26. E. Segal et al., Nature Genet. 34, 166 (2003).
27. A. Hartemink, D. Gifford, T. S. Jaakkola, R. A. Young, Pac. Symp. Biocomput. 6, 422 (2001).
28. S. Imoto, T. Goto, S. Miyano, Pac. Symp. Biocomput. 7, 17S (2002).
29. H. Toh, K. Horimoto, Bioinformatics 18, 287 (2002).
30. T. R. Hughes et al., Cell 102, 109 (2000).
31. S. Shen-Orr, R. Milo, S. Mangan, U. Alon, Nature Genet. 31, 64 (2002).
32. G. Cooper, C. Yoo, Proceedings of the 15th Conference on Uncertainty in Artificial Intelligence, K. Laskey, H. Prade, Eds. (Morgan Kaufmann, San Francisco, 1999), pp. 116-125.
33. I. Ong, J. Glasner, D. Page, Bioinformatics 18 (suppl. 1), S241 (2002).
34. S. Y. Kim, S. Imoto, S. Miyano, Brief. Bioinform. 4, 228 (2003).
35. B. E. Perrin et al., Bioinformatics 19 (suppl. 2), 11138 (2003).
36. A. J. Hartemink, D. K. Gifford, T. S. Jaakkola, R. A. Young, Pac. Symp. Biocomput. 7, 437 (2002).
37. Y. Tamada et al., Bioinformatics 19 (suppl. 2), 11227 (2003).
38. T. Ideker, O. Ozier, B. Schwikowski, A. Siegel, Bioinformatics 18 (suppl. 1), S233 (2002).
39. C. H. Yeang, T. Jaakkola, Proceedings of the 7th Annual International Conference on Computational Molecular Biology, M. Vingron et al., Eds. (ACM Press, New York, 2003), pp. 312-321.
40. H. H. McAdams, A. Arkin, Proc. Natl. Acad. Sci. U.S.A. 94, 814 (1997).
41. W. Vance, A. Arkin, J. Ross, Proc. Natl. Acad. Sci. U.S.A. 99, 5816 (2002).
42. M. Ashburner et al., Nature Genet. 25, 25 (2000).
43. I thank L. Garwin, R. Nelken, D. Pe'er, A. Regev, and I. Wapinski for useful comments on earlier versions of this manuscript, and N. Kaminski, I. Nachman, D. Pe'er, A. Regev, E. Segal, and in particular D. Koller for many insightful discussions. Supported by the Bauer Center for Genomics Research, Harvard University, and a grant from the Israel Science Foundation.